Transcriptomics unlocked evolutional differentiation of photosynthesis and starch metabolism from wild progenitor to cultivars in cassava (Manihot esculenta Crantz)
Zhiqing Xia1,2,*, Xin Chen1,2*, Meiling Zou1,2,ShujuanWang1,2, Yang Zhang1,2, Kun Pan1,2, Xincheng Zhou1,2, Cheng Lu1,2, and Wenquan Wang1,2*
1) The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, PR China
2) Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
*Corresponding authors:
#These authors contributed equally to this work.
Cassava is a typical tropical crop known as high biomass and starch accumulation based on efficient photosynthesis and carbonhydrates transport. However, there is less knowledge on how the mechanisms acquired from the ancestor to the modern varieties that involved in the evolutionary processes. Here, we investigated the transcriptional differences in various tissues between cultivated cassava Arg7 (Manihot esculenta) and its wild progenitor W14 (Manihot flabellifolia).Eight cDNA libraries derived from different tissues of Arg7 and W14 were sequenced by using a Hiseq2000 sequencing system, and 41,302 assembled transcripts were obtained. A total of 25,961 of these transcripts had ≥3 fragments per kilobase per million reads in at least one library. More than 10,000 transcripts were annotated and assigned to 360 metabolic pathways. DEGseq, which identified differentially expressed genes from RNA-Seq data, was used to analyze the transcriptional differences. Significant differences in expression levels in Arg7 and W14 leaves, stems and storage roots were observed between 7.5% and 15.0% of the transcripts. These differentially expressed genes were mainly involved in photosynthesis, as well as starch and sucrose metabolism and other metabolic pathways. Most photosynthesis-related genes and some key starch metabolism-related genes were significantly more expressed in cultivated than wild cassava, which could explain the more efficient photosynthesis and greater starch accumulation in the former. We further investigate the transcriptional regulation of photosynthesis, starch metabolism, and sugar transport gene regulation networks. The network includes 4498 genes. This study is the first time using transcriptional gene regulation network to study the photosynthesis, sugar transport, and starch metabolism in cassava leaves, stems and roots. We compared the transcriptome of cultivated cassava and that of its wild progenitor. Some differentially expressed genes involved in photosynthesis and starch accumulation were identified from the assembled transcripts. These RNA-Seq data might be useful for further studies on gene expression and functional genomics and should facilitate study of the evolution from wild type (C3) to the cultivated cassava (C3-C4 intermediate) in genus Manihot.
Key Words: Cassava, transcriptome, photosynthesis, starch biosynthesis, evolution